MAGeCKFlute - Functional enrichment analysis in MAGeCKFlute
Binbin Wang, Wubing Zhang, Feizhen Wu, Wei Li & X. Shirley Liu
Abstract
The high-throughput CRISPR screens, including knockout and activation/inhibition screens, has revolutionized investigation of gene functions in a wide array of scientific domains, such as somatic cell reprogramming, stem cell differentiation, tumor development/progression, and drug response. It has created computational challenges, such as how to identify the robust gene hits and extract biological insight from the identified hits. To address these challenges, we developed MAGeCKFlute, an integrative analysis pipeline for pooled CRISPR functional genetic screens. The method derives its power on hit identification by normalizing the distribution of gene essentiality score. Probing biological insights, we incorporate multiple public available gene sets, including molecular signatures from MsigDB, pathways from KEGG, REACTOME and protein complexes from CORUM and ComplexPortal database. Utilizing the published enrichment analysis methods and hypergeometric test, MAGeCKFlute shows it’s capacity in the identification of essential protein complexes and pathways.
Citation: if you use MAGeCKFlute in published research, please cite: Binbin Wang, Mei Wang, Wubing Zhang. “Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute.” Nature Protocols (2019), doi: 10.1038/s41596-018-0113-7.t
Load the data for enrichment analysis
library(MAGeCKFlute)
data(rra.gene_summary)
df = ReadRRA(rra.gene_summary)
genelist= df$Score
names(genelist) = df$idEnrichment analysis methods
MAGeCKFlute incorporates three enrichment methods, including Over-Representation Test (ORT), Gene Set Enrichment Analysis (GSEA), and Hypergeometric test (HGT). Here, ORT and GSEA are borrowed from R package clusterProfiler.
Hypergeometric test
# Alternative functions EnrichAnalyzer and enrich.HGT.
hgtRes1 = EnrichAnalyzer(genelist[genelist< -1], method = "HGT")
head(hgtRes1@result)## ID
## REACTOME_72163 REACTOME_72163
## REACTOME_6791226 REACTOME_6791226
## KEGG_hsa03040 KEGG_hsa03040
## GO_VIRAL_GENE_EXPRESSION GO_VIRAL_GENE_EXPRESSION
## REACTOME_9010553 REACTOME_9010553
## GO_RNA_3_END_PROCESSING GO_RNA_3_END_PROCESSING
## Description
## REACTOME_72163 mRNA Splicing - Major Pathway
## REACTOME_6791226 Major pathway of rRNA processing in the nucleolus and cytosol
## KEGG_hsa03040 Spliceosome
## GO_VIRAL_GENE_EXPRESSION VIRAL GENE EXPRESSION
## REACTOME_9010553 Regulation of expression of SLITs and ROBOs
## GO_RNA_3_END_PROCESSING RNA 3 END PROCESSING
## NES pvalue p.adjust GeneRatio
## REACTOME_72163 -16.13486 1.679967e-28 2.309955e-25 49/183
## REACTOME_6791226 -15.58513 2.793384e-24 1.920452e-21 45/186
## KEGG_hsa03040 -13.07523 5.633499e-18 2.582021e-15 34/149
## GO_VIRAL_GENE_EXPRESSION -13.33898 1.272698e-17 4.374899e-15 38/191
## REACTOME_9010553 -13.51965 8.280930e-17 2.277256e-14 35/171
## GO_RNA_3_END_PROCESSING -12.46675 2.695796e-16 6.177866e-14 32/148
## BgRatio
## REACTOME_72163 183/183
## REACTOME_6791226 186/186
## KEGG_hsa03040 149/149
## GO_VIRAL_GENE_EXPRESSION 191/191
## REACTOME_9010553 171/177
## GO_RNA_3_END_PROCESSING 148/148
## geneID
## REACTOME_72163 10772/7536/23020/55339/23517/1479/25804/5094/5433/3192/9343/57819/56949/6632/1665/3312/1660/10262/9775/51585/51593/23451/6426/4686/3191/5430/29894/56259/22938/8175/27339/6428/27316/23398/5434/10286/10523/6625/54883/7307/5435/51340/10992/84950/5438/6626/5440/27258/10713
## REACTOME_6791226 81887/6122/9045/5394/55127/23481/6193/92856/23517/83732/6202/79050/10969/84916/51388/6188/6224/9136/5393/6187/6207/6194/6222/79897/56915/6205/11056/6209/55720/2091/6234/11340/54512/6135/4691/54555/23521/57418/6168/51602/23160/51013/6232/118460/6147
## KEGG_hsa03040 10772/23020/25804/3192/9343/57819/56949/6632/1665/3312/55119/10262/9775/23451/6426/4686/1659/56259/22938/8175/27339/6428/27316/9984/10286/10523/6625/7307/51340/10992/84950/6626/27258/10713
## GO_VIRAL_GENE_EXPRESSION 6122/9150/9045/8661/6193/5094/5433/6202/6188/6224/6187/4927/25920/6207/6194/1660/6222/6598/5702/6205/1025/6209/5430/22938/6234/6135/2959/5434/23521/6168/5435/23435/6232/5438/23279/7936/5440/6147
## REACTOME_9010553 6122/9045/5684/6193/6923/5692/6202/5686/6188/6224/5695/5691/5689/9978/6187/5708/6207/6194/6222/5688/9775/5714/5718/5702/10213/6205/6209/4686/6234/8453/6135/23521/6168/6232/6147
## GO_RNA_3_END_PROCESSING 3028/55339/1479/134353/5433/51728/10212/5393/80145/60528/170506/56915/9775/1025/51585/6426/4686/55656/54931/29894/2091/580/6428/11340/114034/54512/9984/64852/7307/7936/6626/118460
## geneName
## REACTOME_72163 SRSF10/SF1/SNRNP200/WDR33/SKIV2L2/CSTF3/LSM4/PCBP2/POLR2D/HNRNPU/EFTUD2/LSM2/XAB2/SNRPD/DHX15/HSPA8/DHX9/SF3B4/EIF4A3/PCF11/SRRT/SF3B1/SRSF1/NCBP1/HNRNPL/POLR2A/CPSF1/CTNNBL1/SNW1/SF3A2/PRPF19/SRSF3/RBMX/PPWD1/POLR2E/BCAS2/CHERP/SNRNP70/CWC25/U2AF1/POLR2F/CRNKL1/SF3B2/PRPF38A/POLR2I/SNRPA/POLR2K/LSM3/USP39
## REACTOME_6791226 LAS1L/RPL3/RPL14/EXOSC10/HEATR1/PES1/RPS5/IMP4/SKIV2L2/RIOK1/RPS8/NOC4L/EBNA1BP2/CIRH1A/NIP7/RPS3/RPS20/RRP9/EXOSC9/RPS2/RPS13/RPS6/RPS18/RPP21/EXOSC5/RPS11/DDX52/RPS15/TSR1/FBL/RPS28/EXOSC8/EXOSC4/RPL11/NCL/DDX49/RPL13A/WDR18/RPL37A/NOP58/WDR43/EXOSC1/RPS27/EXOSC6/RPL23A
## KEGG_hsa03040 SRSF10/SNRNP200/LSM4/HNRNPU/EFTUD2/LSM2/XAB2/SNRPD/DHX15/HSPA8/PRPF38B/SF3B4/EIF4A3/SF3B1/SRSF1/NCBP1/DHX8/CTNNBL1/SNW1/SF3A2/PRPF19/SRSF3/RBMX/THOC1/BCAS2/CHERP/SNRNP70/U2AF1/CRNKL1/SF3B2/PRPF38A/SNRPA/LSM3/USP39
## GO_VIRAL_GENE_EXPRESSION RPL3/CTDP1/RPL14/EIF3/RPS5/PCBP2/POLR2D/RPS8/RPS3/RPS20/RPS2/NUP88/COBRA1/RPS13/RPS6/DHX9/RPS18/SMARCB1/PSMC3/RPS11/CDK9/RPS15/POLR2A/SNW1/RPS28/RPL11/GTF2B/POLR2E/RPL13A/RPL37A/POLR2F/TARDBP/RPS27/POLR2I/NUP160/RDBP/POLR2K/RPL23A
## REACTOME_9010553 RPL3/RPL14/PSMA3/RPS5/TCEB2/PSMB4/RPS8/PSMA5/RPS3/RPS20/PSMB7/PSMB3/PSMB1/RBX1/RPS2/PSMD2/RPS13/RPS6/RPS18/PSMA7/EIF4A3/PSMD8/PSMD12/PSMC3/PSMD14/RPS11/RPS15/NCBP1/RPS28/CUL2/RPL11/RPL13A/RPL37A/RPS27/RPL23A
## GO_RNA_3_END_PROCESSING HSD17B10/WDR33/CSTF3/LSM11/POLR2D/POLR3K/DDX39/EXOSC9/THOC7/ELAC2/DHX36/EXOSC5/EIF4A3/CDK9/PCF11/SRSF1/NCBP1/INTS8/RG9MTD1/CPSF1/FBL/BARD1/SRSF3/EXOSC8/TOE1/EXOSC4/THOC1/TUT1/U2AF1/RDBP/SNRPA/EXOSC6
## Count
## REACTOME_72163 49
## REACTOME_6791226 45
## KEGG_hsa03040 34
## GO_VIRAL_GENE_EXPRESSION 38
## REACTOME_9010553 35
## GO_RNA_3_END_PROCESSING 32hgtRes2 = enrich.HGT(genelist[genelist< -1])
head(hgtRes2@result)## ID
## GO_VIRAL_GENE_EXPRESSION GO_VIRAL_GENE_EXPRESSION
## GO_RNA_3_END_PROCESSING GO_RNA_3_END_PROCESSING
## GO_TRNA_METABOLIC_PROCESS GO_TRNA_METABOLIC_PROCESS
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION
## GO_MITOCHONDRIAL_GENE_EXPRESSION GO_MITOCHONDRIAL_GENE_EXPRESSION
## GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS
## Description
## GO_VIRAL_GENE_EXPRESSION VIRAL GENE EXPRESSION
## GO_RNA_3_END_PROCESSING RNA 3 END PROCESSING
## GO_TRNA_METABOLIC_PROCESS TRNA METABOLIC PROCESS
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION DNA TEMPLATED TRANSCRIPTION TERMINATION
## GO_MITOCHONDRIAL_GENE_EXPRESSION MITOCHONDRIAL GENE EXPRESSION
## GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS RIBOSOMAL LARGE SUBUNIT BIOGENESIS
## NES pvalue
## GO_VIRAL_GENE_EXPRESSION -13.33898 1.609382e-16
## GO_RNA_3_END_PROCESSING -12.46675 2.400144e-15
## GO_TRNA_METABOLIC_PROCESS -14.96196 3.315299e-15
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION -11.23635 2.044689e-14
## GO_MITOCHONDRIAL_GENE_EXPRESSION -12.22970 2.658660e-14
## GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS -10.52934 8.146541e-14
## p.adjust GeneRatio BgRatio
## GO_VIRAL_GENE_EXPRESSION 1.541788e-13 38/191 191/191
## GO_RNA_3_END_PROCESSING 1.058686e-12 32/148 148/148
## GO_TRNA_METABOLIC_PROCESS 1.058686e-12 35/178 178/178
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION 4.897031e-12 22/74 74/74
## GO_MITOCHONDRIAL_GENE_EXPRESSION 5.093993e-12 32/160 160/160
## GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS 1.231939e-11 21/71 71/71
## geneID
## GO_VIRAL_GENE_EXPRESSION 6122/9150/9045/8661/6193/5094/5433/6202/6188/6224/6187/4927/25920/6207/6194/1660/6222/6598/5702/6205/1025/6209/5430/22938/6234/6135/2959/5434/23521/6168/5435/23435/6232/5438/23279/7936/5440/6147
## GO_RNA_3_END_PROCESSING 3028/55339/1479/134353/5433/51728/10212/5393/80145/60528/170506/56915/9775/1025/51585/6426/4686/55656/54931/29894/2091/580/6428/11340/114034/54512/9984/64852/7307/7936/6626/118460
## GO_TRNA_METABOLIC_PROCESS 7407/54938/3028/55226/3035/8565/348180/10056/51520/1615/51637/51067/57176/25973/51728/112858/79587/60528/79897/27304/285381/10248/51367/90353/2193/51504/55140/54931/29894/4677/283989/57505/112970/92935/55699
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION 2068/55339/64425/1479/134353/84172/51728/9013/1660/25885/51585/10419/4686/5430/29894/2967/5434/7270/404672/5435/6908/5440
## GO_MITOCHONDRIAL_GENE_EXPRESSION 65005/3028/10102/3035/116540/85476/26164/63875/51067/26284/65003/60528/5018/63931/55168/26589/90480/28973/28998/29093/51335/6182/54931/3396/64981/7019/57505/55699/116541/51081/51021/5442
## GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS 81887/6122/9045/23481/56342/4839/10969/51388/23195/54475/26156/65003/3692/51491/51187/6135/57418/9875/23560/55651/6147
## geneName
## GO_VIRAL_GENE_EXPRESSION RPL3/CTDP1/RPL14/EIF3/RPS5/PCBP2/POLR2D/RPS8/RPS3/RPS20/RPS2/NUP88/COBRA1/RPS13/RPS6/DHX9/RPS18/SMARCB1/PSMC3/RPS11/CDK9/RPS15/POLR2A/SNW1/RPS28/RPL11/GTF2B/POLR2E/RPL13A/RPL37A/POLR2F/TARDBP/RPS27/POLR2I/NUP160/RDBP/POLR2K/RPL23A
## GO_RNA_3_END_PROCESSING HSD17B10/WDR33/CSTF3/LSM11/POLR2D/POLR3K/DDX39/EXOSC9/THOC7/ELAC2/DHX36/EXOSC5/EIF4A3/CDK9/PCF11/SRSF1/NCBP1/INTS8/RG9MTD1/CPSF1/FBL/BARD1/SRSF3/EXOSC8/TOE1/EXOSC4/THOC1/TUT1/U2AF1/RDBP/SNRPA/EXOSC6
## GO_TRNA_METABOLIC_PROCESS VARS/SYS/HSD17B10/NAT10/HARS/YARS/CTU2/FARSB/LARS/DARS/C14orf166/YARS2/VARS2/PARS2/POLR3K/TP53RK/CARS2/ELAC2/RPP21/MOCS3/DPH3/POP7/POP5/CTU1/FARSA/TRMT112/ELP3/RG9MTD1/CPSF1/NARS/TSEN54/AARS2/KTI12/MARS2/IARS2
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION ERCC2/WDR33/POLR1E/CSTF3/LSM11/POLR1B/POLR3K/TAF1C/DHX9/POLR1A/PCF11/PRMT5/NCBP1/POLR2A/CPSF1/GTF2H3/POLR2E/TTF1/GTF2H5/POLR2F/TBP/POLR2K
## GO_MITOCHONDRIAL_GENE_EXPRESSION MRPL9/HSD17B10/TSFM/HARS/MRPL53/GFM1/GTPBP5/MRPL17/YARS2/ERAL1/MRPL11/ELAC2/OXA1L/MRPS14/MRPS18A/MRPL46/GADD45GIP1/MRPS18B/MRPL13/MRPL22/NGRN/MRPL12/RG9MTD1/ICT1/MRPL34/TFAM/AARS2/IARS2/MRPL54/MRPS7/MRPS16/POLRMT
## GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS LAS1L/RPL3/RPL14/PES1/PPAN/NOL1/EBNA1BP2/NIP7/MDN1/NLE1/RSL1D1/MRPL11/EIF6/NOP16/RSL24D1/RPL11/WDR18/URB1/GTPBP4/NHP2/RPL23A
## Count
## GO_VIRAL_GENE_EXPRESSION 38
## GO_RNA_3_END_PROCESSING 32
## GO_TRNA_METABOLIC_PROCESS 35
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION 22
## GO_MITOCHONDRIAL_GENE_EXPRESSION 32
## GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS 21Over-representation test
# Alternative functions EnrichAnalyzer and enrich.ORT.
ortRes1 = EnrichAnalyzer(genelist[genelist< -1], method = "ORT")
head(ortRes1@result)## ID
## REACTOME_72163 REACTOME_72163
## REACTOME_6791226 REACTOME_6791226
## KEGG_hsa03040 KEGG_hsa03040
## GO_VIRAL_GENE_EXPRESSION GO_VIRAL_GENE_EXPRESSION
## REACTOME_9010553 REACTOME_9010553
## GO_TRNA_METABOLIC_PROCESS GO_TRNA_METABOLIC_PROCESS
## Description
## REACTOME_72163 mRNA Splicing - Major Pathway
## REACTOME_6791226 Major pathway of rRNA processing in the nucleolus and cytosol
## KEGG_hsa03040 Spliceosome
## GO_VIRAL_GENE_EXPRESSION VIRAL GENE EXPRESSION
## REACTOME_9010553 Regulation of expression of SLITs and ROBOs
## GO_TRNA_METABOLIC_PROCESS TRNA METABOLIC PROCESS
## NES pvalue p.adjust GeneRatio
## REACTOME_72163 -16.13486 8.710479e-29 3.180196e-25 49/566
## REACTOME_6791226 -15.58513 1.690300e-24 3.085643e-21 45/566
## KEGG_hsa03040 -13.07523 6.231834e-18 7.584142e-15 34/566
## GO_VIRAL_GENE_EXPRESSION -13.33898 9.917202e-18 9.051926e-15 38/566
## REACTOME_9010553 -13.51965 7.848460e-17 5.730946e-14 35/566
## GO_TRNA_METABOLIC_PROCESS -14.96196 2.940048e-16 1.663592e-13 35/566
## BgRatio
## REACTOME_72163 183/15323
## REACTOME_6791226 186/15323
## KEGG_hsa03040 149/15323
## GO_VIRAL_GENE_EXPRESSION 191/15323
## REACTOME_9010553 171/15323
## GO_TRNA_METABOLIC_PROCESS 178/15323
## geneID
## REACTOME_72163 10772/7536/23020/55339/23517/1479/25804/5094/5433/3192/9343/57819/56949/6632/1665/3312/1660/10262/9775/51585/51593/23451/6426/4686/3191/5430/29894/56259/22938/8175/27339/6428/27316/23398/5434/10286/10523/6625/54883/7307/5435/51340/10992/84950/5438/6626/5440/27258/10713
## REACTOME_6791226 81887/6122/9045/5394/55127/23481/6193/92856/23517/83732/6202/79050/10969/84916/51388/6188/6224/9136/5393/6187/6207/6194/6222/79897/56915/6205/11056/6209/55720/2091/6234/11340/54512/6135/4691/54555/23521/57418/6168/51602/23160/51013/6232/118460/6147
## KEGG_hsa03040 10772/23020/25804/3192/9343/57819/56949/6632/1665/3312/55119/10262/9775/23451/6426/4686/1659/56259/22938/8175/27339/6428/27316/9984/10286/10523/6625/7307/51340/10992/84950/6626/27258/10713
## GO_VIRAL_GENE_EXPRESSION 6122/9150/9045/8661/6193/5094/5433/6202/6188/6224/6187/4927/25920/6207/6194/1660/6222/6598/5702/6205/1025/6209/5430/22938/6234/6135/2959/5434/23521/6168/5435/23435/6232/5438/23279/7936/5440/6147
## REACTOME_9010553 6122/9045/5684/6193/6923/5692/6202/5686/6188/6224/5695/5691/5689/9978/6187/5708/6207/6194/6222/5688/9775/5714/5718/5702/10213/6205/6209/4686/6234/8453/6135/23521/6168/6232/6147
## GO_TRNA_METABOLIC_PROCESS 7407/54938/3028/55226/3035/8565/348180/10056/51520/1615/51637/51067/57176/25973/51728/112858/79587/60528/79897/27304/285381/10248/51367/90353/2193/51504/55140/54931/29894/4677/283989/57505/112970/92935/55699
## geneName
## REACTOME_72163 SRSF10/SF1/SNRNP200/WDR33/MTREX/CSTF3/LSM4/PCBP2/POLR2D/HNRNPU/EFTUD2/LSM2/XAB2/SNRPD1/DHX15/HSPA8/DHX9/SF3B4/EIF4A3/PCF11/SRRT/SF3B1/SRSF1/NCBP1/HNRNPL/POLR2A/CPSF1/CTNNBL1/SNW1/SF3A2/PRPF19/SRSF3/RBMX/PPWD1/POLR2E/BCAS2/CHERP/SNRNP70/CWC25/U2AF1/POLR2F/CRNKL1/SF3B2/PRPF38A/POLR2I/SNRPA/POLR2K/LSM3/USP39
## REACTOME_6791226 LAS1L/RPL3/RPL14/EXOSC10/HEATR1/PES1/RPS5/IMP4/MTREX/RIOK1/RPS8/NOC4L/EBNA1BP2/UTP4/NIP7/RPS3/RPS20/RRP9/EXOSC9/RPS2/RPS13/RPS6/RPS18/RPP21/EXOSC5/RPS11/DDX52/RPS15/TSR1/FBL/RPS28/EXOSC8/EXOSC4/RPL11/NCL/DDX49/RPL13A/WDR18/RPL37A/NOP58/WDR43/EXOSC1/RPS27/EXOSC6/RPL23A
## KEGG_hsa03040 SRSF10/SNRNP200/LSM4/HNRNPU/EFTUD2/LSM2/XAB2/SNRPD1/DHX15/HSPA8/PRPF38B/SF3B4/EIF4A3/SF3B1/SRSF1/NCBP1/DHX8/CTNNBL1/SNW1/SF3A2/PRPF19/SRSF3/RBMX/THOC1/BCAS2/CHERP/SNRNP70/U2AF1/CRNKL1/SF3B2/PRPF38A/SNRPA/LSM3/USP39
## GO_VIRAL_GENE_EXPRESSION RPL3/CTDP1/RPL14/EIF3A/RPS5/PCBP2/POLR2D/RPS8/RPS3/RPS20/RPS2/NUP88/NELFB/RPS13/RPS6/DHX9/RPS18/SMARCB1/PSMC3/RPS11/CDK9/RPS15/POLR2A/SNW1/RPS28/RPL11/GTF2B/POLR2E/RPL13A/RPL37A/POLR2F/TARDBP/RPS27/POLR2I/NUP160/NELFE/POLR2K/RPL23A
## REACTOME_9010553 RPL3/RPL14/PSMA3/RPS5/ELOB/PSMB4/RPS8/PSMA5/RPS3/RPS20/PSMB7/PSMB3/PSMB1/RBX1/RPS2/PSMD2/RPS13/RPS6/RPS18/PSMA7/EIF4A3/PSMD8/PSMD12/PSMC3/PSMD14/RPS11/RPS15/NCBP1/RPS28/CUL2/RPL11/RPL13A/RPL37A/RPS27/RPL23A
## GO_TRNA_METABOLIC_PROCESS VARS1/SARS2/HSD17B10/NAT10/HARS1/YARS1/CTU2/FARSB/LARS1/DARS1/RTRAF/YARS2/VARS2/PARS2/POLR3K/TP53RK/CARS2/ELAC2/RPP21/MOCS3/DPH3/POP7/POP5/CTU1/FARSA/TRMT112/ELP3/TRMT10C/CPSF1/NARS1/TSEN54/AARS2/KTI12/MARS2/IARS2
## Count
## REACTOME_72163 49
## REACTOME_6791226 45
## KEGG_hsa03040 34
## GO_VIRAL_GENE_EXPRESSION 38
## REACTOME_9010553 35
## GO_TRNA_METABOLIC_PROCESS 35ortRes2 = enrich.ORT(genelist[genelist< -1])
head(ortRes2@result)## ID
## GO_VIRAL_GENE_EXPRESSION GO_VIRAL_GENE_EXPRESSION
## GO_TRNA_METABOLIC_PROCESS GO_TRNA_METABOLIC_PROCESS
## GO_RNA_3_END_PROCESSING GO_RNA_3_END_PROCESSING
## GO_MITOCHONDRIAL_GENE_EXPRESSION GO_MITOCHONDRIAL_GENE_EXPRESSION
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION
## GO_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION GO_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION
## Description
## GO_VIRAL_GENE_EXPRESSION VIRAL GENE EXPRESSION
## GO_TRNA_METABOLIC_PROCESS TRNA METABOLIC PROCESS
## GO_RNA_3_END_PROCESSING RNA 3 END PROCESSING
## GO_MITOCHONDRIAL_GENE_EXPRESSION MITOCHONDRIAL GENE EXPRESSION
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION DNA TEMPLATED TRANSCRIPTION TERMINATION
## GO_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION DNA TEMPLATED TRANSCRIPTION ELONGATION
## NES pvalue
## GO_VIRAL_GENE_EXPRESSION -13.33898 3.588697e-17
## GO_TRNA_METABOLIC_PROCESS -14.96196 9.604968e-16
## GO_RNA_3_END_PROCESSING -12.46675 9.629787e-16
## GO_MITOCHONDRIAL_GENE_EXPRESSION -12.22970 1.015077e-14
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION -11.23635 2.764538e-14
## GO_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION -11.23327 6.621957e-14
## p.adjust GeneRatio
## GO_VIRAL_GENE_EXPRESSION 9.445451e-14 38/545
## GO_TRNA_METABOLIC_PROCESS 8.448533e-13 35/545
## GO_RNA_3_END_PROCESSING 8.448533e-13 32/545
## GO_MITOCHONDRIAL_GENE_EXPRESSION 6.679206e-12 32/545
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION 1.455253e-11 22/545
## GO_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION 2.904832e-11 26/545
## BgRatio
## GO_VIRAL_GENE_EXPRESSION 191/14168
## GO_TRNA_METABOLIC_PROCESS 178/14168
## GO_RNA_3_END_PROCESSING 148/14168
## GO_MITOCHONDRIAL_GENE_EXPRESSION 160/14168
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION 74/14168
## GO_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION 111/14168
## geneID
## GO_VIRAL_GENE_EXPRESSION 6122/9150/9045/8661/6193/5094/5433/6202/6188/6224/6187/4927/25920/6207/6194/1660/6222/6598/5702/6205/1025/6209/5430/22938/6234/6135/2959/5434/23521/6168/5435/23435/6232/5438/23279/7936/5440/6147
## GO_TRNA_METABOLIC_PROCESS 7407/54938/3028/55226/3035/8565/348180/10056/51520/1615/51637/51067/57176/25973/51728/112858/79587/60528/79897/27304/285381/10248/51367/90353/2193/51504/55140/54931/29894/4677/283989/57505/112970/92935/55699
## GO_RNA_3_END_PROCESSING 3028/55339/1479/134353/5433/51728/10212/5393/80145/60528/170506/56915/9775/1025/51585/6426/4686/55656/54931/29894/2091/580/6428/11340/114034/54512/9984/64852/7307/7936/6626/118460
## GO_MITOCHONDRIAL_GENE_EXPRESSION 65005/3028/10102/3035/116540/85476/26164/63875/51067/26284/65003/60528/5018/63931/55168/26589/90480/28973/28998/29093/51335/6182/54931/3396/64981/7019/57505/55699/116541/51081/51021/5442
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION 2068/55339/64425/1479/134353/84172/51728/9013/1660/25885/51585/10419/4686/5430/29894/2967/5434/7270/404672/5435/6908/5440
## GO_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION 9150/2068/10102/64425/6923/5433/3192/84172/9013/25920/25885/23168/1025/55140/8178/4686/5430/9984/2967/5434/404672/5435/5438/6908/7936/5440
## geneName
## GO_VIRAL_GENE_EXPRESSION RPL3/CTDP1/RPL14/EIF3A/RPS5/PCBP2/POLR2D/RPS8/RPS3/RPS20/RPS2/NUP88/NELFB/RPS13/RPS6/DHX9/RPS18/SMARCB1/PSMC3/RPS11/CDK9/RPS15/POLR2A/SNW1/RPS28/RPL11/GTF2B/POLR2E/RPL13A/RPL37A/POLR2F/TARDBP/RPS27/POLR2I/NUP160/NELFE/POLR2K/RPL23A
## GO_TRNA_METABOLIC_PROCESS VARS1/SARS2/HSD17B10/NAT10/HARS1/YARS1/CTU2/FARSB/LARS1/DARS1/RTRAF/YARS2/VARS2/PARS2/POLR3K/TP53RK/CARS2/ELAC2/RPP21/MOCS3/DPH3/POP7/POP5/CTU1/FARSA/TRMT112/ELP3/TRMT10C/CPSF1/NARS1/TSEN54/AARS2/KTI12/MARS2/IARS2
## GO_RNA_3_END_PROCESSING HSD17B10/WDR33/CSTF3/LSM11/POLR2D/POLR3K/DDX39A/EXOSC9/THOC7/ELAC2/DHX36/EXOSC5/EIF4A3/CDK9/PCF11/SRSF1/NCBP1/INTS8/TRMT10C/CPSF1/FBL/BARD1/SRSF3/EXOSC8/TOE1/EXOSC4/THOC1/PAPD2/U2AF1/NELFE/SNRPA/EXOSC6
## GO_MITOCHONDRIAL_GENE_EXPRESSION MRPL9/HSD17B10/TSFM/HARS1/MRPL53/GFM1/MTG2/MRPL17/YARS2/ERAL1/MRPL11/ELAC2/OXA1L/MRPS14/MRPS18A/MRPL46/GADD45GIP1/MRPS18B/MRPL13/MRPL22/NGRN/MRPL12/TRMT10C/MRPL58/MRPL34/TFAM/AARS2/IARS2/MRPL54/MRPS7/MRPS16/POLRMT
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION ERCC2/WDR33/POLR1E/CSTF3/LSM11/POLR1B/POLR3K/TAF1C/DHX9/POLR1A/PCF11/PRMT5/NCBP1/POLR2A/CPSF1/GTF2H3/POLR2E/TTF1/GTF2H5/POLR2F/TBP/POLR2K
## GO_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION CTDP1/ERCC2/TSFM/POLR1E/ELOB/POLR2D/HNRNPU/POLR1B/TAF1C/NELFB/POLR1A/RTF1/CDK9/ELP3/ELL/NCBP1/POLR2A/THOC1/GTF2H3/POLR2E/GTF2H5/POLR2F/POLR2I/TBP/NELFE/POLR2K
## Count
## GO_VIRAL_GENE_EXPRESSION 38
## GO_TRNA_METABOLIC_PROCESS 35
## GO_RNA_3_END_PROCESSING 32
## GO_MITOCHONDRIAL_GENE_EXPRESSION 32
## GO_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION 22
## GO_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION 26Gene set enrichment analysis
# Alternative functions EnrichAnalyzer and enrich.GSE.
gseRes1 = EnrichAnalyzer(genelist, method = "GSEA")## Warning in fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize, : There are ties in the preranked stats (4.53% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.head(gseRes1@result)## ID
## GO_CELLULAR_KETONE_METABOLIC_PROCESS GO_CELLULAR_KETONE_METABOLIC_PROCESS
## GO_NUCLEAR_EXPORT GO_NUCLEAR_EXPORT
## GO_RESPONSE_TO_INTERLEUKIN_1 GO_RESPONSE_TO_INTERLEUKIN_1
## GO_TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER GO_TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS
## Description
## GO_CELLULAR_KETONE_METABOLIC_PROCESS CELLULAR KETONE METABOLIC PROCESS
## GO_NUCLEAR_EXPORT NUCLEAR EXPORT
## GO_RESPONSE_TO_INTERLEUKIN_1 RESPONSE TO INTERLEUKIN 1
## GO_TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER TRANSCRIPTION INITIATION FROM RNA POLYMERASE II PROMOTER
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN ANTIGEN PROCESSING AND PRESENTATION OF PEPTIDE ANTIGEN
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS REGULATION OF MRNA CATABOLIC PROCESS
## NES
## GO_CELLULAR_KETONE_METABOLIC_PROCESS -1.860256
## GO_NUCLEAR_EXPORT -2.043578
## GO_RESPONSE_TO_INTERLEUKIN_1 -1.855469
## GO_TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER -1.717426
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN -1.979438
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS -2.151959
## pvalue
## GO_CELLULAR_KETONE_METABOLIC_PROCESS 0.0005112474
## GO_NUCLEAR_EXPORT 0.0005112474
## GO_RESPONSE_TO_INTERLEUKIN_1 0.0005112474
## GO_TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER 0.0005112474
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN 0.0005115090
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS 0.0005115090
## p.adjust
## GO_CELLULAR_KETONE_METABOLIC_PROCESS 0.01624632
## GO_NUCLEAR_EXPORT 0.01624632
## GO_RESPONSE_TO_INTERLEUKIN_1 0.01624632
## GO_TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER 0.01624632
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN 0.01624632
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS 0.01624632
## geneID
## GO_CELLULAR_KETONE_METABOLIC_PROCESS 231/2739/5719/5682/23198/2531/5709/10229/10197/5704/8660/5706/5713/57546/5705/5690/27235/5710/9861/5685/5694/5687/51805/10213/7167/5702/5686/5692/5695/5708/5718/5688/5714/2821/2475/5689/5684/5691
## GO_NUCLEAR_EXPORT 10189/6432/9939/79902/10768/6059/5903/10657/811/7884/8683/8189/57122/51512/9147/53981/3921/81608/56943/9972/55746/7175/29072/3181/11097/11261/55781/79228/23212/6396/23293/160419/1434/2733/23511/11338/9818/22794/23144/9785/55341/5976/5310/65083/5905/10250/81929/6428/6209/5781/6426/9984/57510/9775/29894/23381/23279/9887/4686/80145/7307/1660/5784/7295/55339/4927/580/5433/3692
## GO_RESPONSE_TO_INTERLEUKIN_1 5719/5682/23198/1906/5709/10197/5704/5706/5713/7334/5705/7528/5690/5976/5710/9861/5685/5694/5687/10213/5702/5686/5692/5695/5708/5718/27316/5688/5714/6885/5689/9978/23291/5684/5691/6880
## GO_TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER 6877/51616/2961/892/5704/1024/5706/29079/6722/5432/5436/5705/902/112869/5430/6879/126382/5435/112950/9477/2959/5702/404672/1025/6873/5438/5440/90390/51003/9441/2068/83860/5434/170506/2967/5433/6880/6908
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN 811/3109/10332/10120/5707/10437/1785/5719/5682/23198/2210/5709/3832/10121/6396/10197/5704/1062/2923/5706/5713/1639/3796/5705/10540/10671/51164/84516/5690/5710/11004/9861/5685/5694/5687/10213/11258/829/5702/5686/81930/1778/5692/5695/5708/5718/9493/5688/5714/1213/832/24137/5689/5684/5691
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS 6418/90806/8125/1432/5719/5682/23198/23435/9698/1994/22894/8570/5709/10197/55095/5704/5706/5713/79068/51594/5436/5705/56339/23404/5690/5976/29883/5710/5073/9861/5685/5694/5687/1869/56915/10213/5702/5393/5686/3312/51013/3842/5692/5695/5708/118460/1660/23019/5718/5688/5714/2475/170506/54512/5689/57721/3192/54464/11340/5684/5691
## geneName
## GO_CELLULAR_KETONE_METABOLIC_PROCESS AKR1B1/GLO1/PSMD13/PSMA1/PSME4/KDSR/PSMD3/COQ7/PSME3/PSMC4/IRS2/PSMC6/PSMD7/PDP2/PSMC5/PSMB2/COQ2/PSMD4/PSMD6/PSMA4/PSMB6/PSMA6/COQ3/PSMD14/TPI1/PSMC3/PSMA5/PSMB4/PSMB7/PSMD2/PSMD12/PSMA7/PSMD8/GPI/MTOR/PSMB1/PSMA3/PSMB3
## GO_NUCLEAR_EXPORT ALYREF/SRSF7/RBM8A/NUP85/AHCYL1/ABCE1/RANBP2/KHDRBS1/CALR/SLBP/SRSF9/SYMPK/NUP107/GTSE1/NEMF/CPSF2/RPSA/FIP1L1/ENY2/NUP153/NUP133/TPR/SETD2/HNRNPA2B1/NUP42/CHP1/RIOK2/THOC6/RRS1/SEC13/SMG6/C12orf50/CSE1L/GLE1/NUP188/U2AF2/NUP58/CASC3/ZC3H3/DHX38/LSG1/UPF1/PKD1/NOL6/RANGAP1/SRRM1/SEH1L/SRSF3/RPS15/PTPN11/SRSF1/THOC1/XPO5/EIF4A3/CPSF1/SMG5/NUP160/SMG7/NCBP1/THOC7/U2AF1/DHX9/PTPN14/TXN/WDR33/NUP88/BARD1/POLR2D/EIF6
## GO_RESPONSE_TO_INTERLEUKIN_1 PSMD13/PSMA1/PSME4/EDN1/PSMD3/PSME3/PSMC4/PSMC6/PSMD7/UBE2N/PSMC5/YY1/PSMB2/UPF1/PSMD4/PSMD6/PSMA4/PSMB6/PSMA6/PSMD14/PSMC3/PSMA5/PSMB4/PSMB7/PSMD2/PSMD12/RBMX/PSMA7/PSMD8/MAP3K7/PSMB1/RBX1/FBXW11/PSMA3/PSMB3/TAF9
## GO_TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER TAF5/TAF9B/GTF2E2/CCNC/PSMC4/CDK8/PSMC6/MED4/SRF/POLR2C/POLR2G/PSMC5/CCNH/SGF29/POLR2A/TAF7/NR2C2AP/POLR2F/MED8/MED20/GTF2B/PSMC3/GTF2H5/CDK9/TAF2/POLR2I/POLR2K/MED30/MED31/MED26/ERCC2/TAF3/POLR2E/DHX36/GTF2H3/POLR2D/TAF9/TBP
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN CALR/HLA-DMB/CLEC4M/ACTR1B/PSMD1/IFI30/DNM2/PSMD13/PSMA1/PSME4/FCGR1B/PSMD3/KIF11/ACTR1A/SEC13/PSME3/PSMC4/CENPE/PDIA3/PSMC6/PSMD7/DCTN1/KIF2A/PSMC5/DCTN2/DCTN6/DCTN4/DCTN5/PSMB2/PSMD4/KIF2C/PSMD6/PSMA4/PSMB6/PSMA6/PSMD14/DCTN3/CAPZA1/PSMC3/PSMA5/KIF18A/DYNC1H1/PSMB4/PSMB7/PSMD2/PSMD12/KIF23/PSMA7/PSMD8/CLTC/CAPZB/KIF4A/PSMB1/PSMA3/PSMB3
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS SET/ANGEL2/ANP32A/MAPK14/PSMD13/PSMA1/PSME4/TARDBP/PUM1/ELAVL1/DIS3/KHSRP/PSMD3/PSME3/SAMD4B/PSMC4/PSMC6/PSMD7/FTO/NBAS/POLR2G/PSMC5/METTL3/EXOSC2/PSMB2/UPF1/CNOT7/PSMD4/PARN/PSMD6/PSMA4/PSMB6/PSMA6/E2F1/EXOSC5/PSMD14/PSMC3/EXOSC9/PSMA5/HSPA8/EXOSC1/TNPO1/PSMB4/PSMB7/PSMD2/EXOSC6/DHX9/CNOT1/PSMD12/PSMA7/PSMD8/MTOR/DHX36/EXOSC4/PSMB1/METTL14/HNRNPU/XRN1/EXOSC8/PSMA3/PSMB3
## Count
## GO_CELLULAR_KETONE_METABOLIC_PROCESS 38
## GO_NUCLEAR_EXPORT 69
## GO_RESPONSE_TO_INTERLEUKIN_1 36
## GO_TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER 38
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN 55
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS 61gseRes2 = enrich.GSE(genelist)## Warning in fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize, : There are ties in the preranked stats (4.53% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.head(gseRes2@result)## ID
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN
## GO_NUCLEAR_EXPORT GO_NUCLEAR_EXPORT
## GO_RESPONSE_TO_INTERLEUKIN_1 GO_RESPONSE_TO_INTERLEUKIN_1
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS
## GO_CELLULAR_KETONE_METABOLIC_PROCESS GO_CELLULAR_KETONE_METABOLIC_PROCESS
## GO_ESTABLISHMENT_OF_RNA_LOCALIZATION GO_ESTABLISHMENT_OF_RNA_LOCALIZATION
## Description
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN ANTIGEN PROCESSING AND PRESENTATION OF PEPTIDE ANTIGEN
## GO_NUCLEAR_EXPORT NUCLEAR EXPORT
## GO_RESPONSE_TO_INTERLEUKIN_1 RESPONSE TO INTERLEUKIN 1
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS REGULATION OF MRNA CATABOLIC PROCESS
## GO_CELLULAR_KETONE_METABOLIC_PROCESS CELLULAR KETONE METABOLIC PROCESS
## GO_ESTABLISHMENT_OF_RNA_LOCALIZATION ESTABLISHMENT OF RNA LOCALIZATION
## NES
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN -1.985897
## GO_NUCLEAR_EXPORT -2.047290
## GO_RESPONSE_TO_INTERLEUKIN_1 -1.859196
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS -2.155147
## GO_CELLULAR_KETONE_METABOLIC_PROCESS -1.862174
## GO_ESTABLISHMENT_OF_RNA_LOCALIZATION -2.069116
## pvalue
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN 0.0005086470
## GO_NUCLEAR_EXPORT 0.0005086470
## GO_RESPONSE_TO_INTERLEUKIN_1 0.0005089059
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS 0.0005094244
## GO_CELLULAR_KETONE_METABOLIC_PROCESS 0.0005096840
## GO_ESTABLISHMENT_OF_RNA_LOCALIZATION 0.0005096840
## p.adjust
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN 0.02142441
## GO_NUCLEAR_EXPORT 0.02142441
## GO_RESPONSE_TO_INTERLEUKIN_1 0.02142441
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS 0.02142441
## GO_CELLULAR_KETONE_METABOLIC_PROCESS 0.02142441
## GO_ESTABLISHMENT_OF_RNA_LOCALIZATION 0.02142441
## geneID
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN 811/3109/10332/10120/5707/10437/1785/5719/5682/23198/2210/5709/3832/10121/6396/10197/5704/1062/2923/5706/5713/1639/3796/5705/10540/10671/51164/84516/5690/5710/11004/9861/5685/5694/5687/10213/11258/829/5702/5686/81930/1778/5692/5695/5708/5718/9493/5688/5714/1213/832/24137/5689/5684/5691
## GO_NUCLEAR_EXPORT 10189/6432/9939/79902/10768/6059/5903/10657/811/7884/8683/8189/57122/51512/9147/53981/3921/81608/56943/9972/55746/7175/29072/3181/11097/11261/55781/79228/23212/6396/23293/160419/1434/2733/23511/11338/9818/22794/23144/9785/55341/5976/5310/65083/5905/10250/81929/6428/6209/5781/6426/9984/57510/9775/29894/23381/23279/9887/4686/80145/7307/1660/5784/7295/55339/4927/580/5433/3692
## GO_RESPONSE_TO_INTERLEUKIN_1 5719/5682/23198/1906/5709/10197/5704/5706/5713/7334/5705/7528/5690/5976/5710/9861/5685/5694/5687/10213/5702/5686/5692/5695/5708/5718/27316/5688/5714/6885/5689/9978/23291/5684/5691/6880
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS 6418/90806/8125/1432/5719/5682/23198/23435/9698/1994/22894/8570/5709/10197/55095/5704/5706/5713/79068/51594/5436/5705/56339/23404/5690/5976/29883/5710/5073/9861/5685/5694/5687/1869/56915/10213/5702/5393/5686/3312/51013/3842/5692/5695/5708/118460/1660/23019/5718/5688/5714/2475/170506/54512/5689/57721/3192/54464/11340/5684/5691
## GO_CELLULAR_KETONE_METABOLIC_PROCESS 231/2739/5719/5682/23198/2531/5709/10229/10197/5704/8660/5706/5713/57546/5705/5690/27235/5710/9861/5685/5694/5687/51805/10213/7167/5702/5686/5692/5695/5708/5718/5688/5714/2821/2475/5689/5684/5691
## GO_ESTABLISHMENT_OF_RNA_LOCALIZATION 10189/6432/9939/79902/6059/5903/10657/7884/8683/8189/57122/53981/3921/387990/81608/56943/5813/9972/8570/9793/3297/55746/7175/29072/3181/11097/55781/29074/79228/23212/6396/7048/23293/160419/545/2733/23511/11338/9818/22794/23144/9785/5976/65083/10250/81929/6428/6209/6426/9984/57510/9775/29894/23381/23279/9887/9804/4686/80145/7307/1660/55339/51637/4927/7014/3192/5433/6421/3692
## geneName
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN CALR/HLA-DMB/CLEC4M/ACTR1B/PSMD1/IFI30/DNM2/PSMD13/PSMA1/PSME4/FCGR1B/PSMD3/KIF11/ACTR1A/SEC13/PSME3/PSMC4/CENPE/PDIA3/PSMC6/PSMD7/DCTN1/KIF2A/PSMC5/DCTN2/DCTN6/DCTN4/DCTN5/PSMB2/PSMD4/KIF2C/PSMD6/PSMA4/PSMB6/PSMA6/PSMD14/DCTN3/CAPZA1/PSMC3/PSMA5/KIF18A/DYNC1H1/PSMB4/PSMB7/PSMD2/PSMD12/KIF23/PSMA7/PSMD8/CLTC/CAPZB/KIF4A/PSMB1/PSMA3/PSMB3
## GO_NUCLEAR_EXPORT ALYREF/SRSF7/RBM8A/NUP85/AHCYL1/ABCE1/RANBP2/KHDRBS1/CALR/SLBP/SRSF9/SYMPK/NUP107/GTSE1/NEMF/CPSF2/RPSA/FIP1L1/ENY2/NUP153/NUP133/TPR/SETD2/HNRNPA2B1/NUP42/CHP1/RIOK2/THOC6/RRS1/SEC13/SMG6/C12orf50/CSE1L/GLE1/NUP188/U2AF2/NUP58/CASC3/ZC3H3/DHX38/LSG1/UPF1/PKD1/NOL6/RANGAP1/SRRM1/SEH1L/SRSF3/RPS15/PTPN11/SRSF1/THOC1/XPO5/EIF4A3/CPSF1/SMG5/NUP160/SMG7/NCBP1/THOC7/U2AF1/DHX9/PTPN14/TXN/WDR33/NUP88/BARD1/POLR2D/EIF6
## GO_RESPONSE_TO_INTERLEUKIN_1 PSMD13/PSMA1/PSME4/EDN1/PSMD3/PSME3/PSMC4/PSMC6/PSMD7/UBE2N/PSMC5/YY1/PSMB2/UPF1/PSMD4/PSMD6/PSMA4/PSMB6/PSMA6/PSMD14/PSMC3/PSMA5/PSMB4/PSMB7/PSMD2/PSMD12/RBMX/PSMA7/PSMD8/MAP3K7/PSMB1/RBX1/FBXW11/PSMA3/PSMB3/TAF9
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS SET/ANGEL2/ANP32A/MAPK14/PSMD13/PSMA1/PSME4/TARDBP/PUM1/ELAVL1/DIS3/KHSRP/PSMD3/PSME3/SAMD4B/PSMC4/PSMC6/PSMD7/FTO/NBAS/POLR2G/PSMC5/METTL3/EXOSC2/PSMB2/UPF1/CNOT7/PSMD4/PARN/PSMD6/PSMA4/PSMB6/PSMA6/E2F1/EXOSC5/PSMD14/PSMC3/EXOSC9/PSMA5/HSPA8/EXOSC1/TNPO1/PSMB4/PSMB7/PSMD2/EXOSC6/DHX9/CNOT1/PSMD12/PSMA7/PSMD8/MTOR/DHX36/EXOSC4/PSMB1/METTL14/HNRNPU/XRN1/EXOSC8/PSMA3/PSMB3
## GO_CELLULAR_KETONE_METABOLIC_PROCESS AKR1B1/GLO1/PSMD13/PSMA1/PSME4/KDSR/PSMD3/COQ7/PSME3/PSMC4/IRS2/PSMC6/PSMD7/PDP2/PSMC5/PSMB2/COQ2/PSMD4/PSMD6/PSMA4/PSMB6/PSMA6/COQ3/PSMD14/TPI1/PSMC3/PSMA5/PSMB4/PSMB7/PSMD2/PSMD12/PSMA7/PSMD8/GPI/MTOR/PSMB1/PSMA3/PSMB3
## GO_ESTABLISHMENT_OF_RNA_LOCALIZATION ALYREF/SRSF7/RBM8A/NUP85/ABCE1/RANBP2/KHDRBS1/SLBP/SRSF9/SYMPK/NUP107/CPSF2/RPSA/TOMM20L/FIP1L1/ENY2/PURA/NUP153/KHSRP/CKAP5/HSF1/NUP133/TPR/SETD2/HNRNPA2B1/NUP42/RIOK2/MRPL18/THOC6/RRS1/SEC13/TGFBR2/SMG6/C12orf50/ATR/GLE1/NUP188/U2AF2/NUP58/CASC3/ZC3H3/DHX38/UPF1/NOL6/SRRM1/SEH1L/SRSF3/RPS15/SRSF1/THOC1/XPO5/EIF4A3/CPSF1/SMG5/NUP160/SMG7/TOMM20/NCBP1/THOC7/U2AF1/DHX9/WDR33/RTRAF/NUP88/TERF2/HNRNPU/POLR2D/SFPQ/EIF6
## Count
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN 55
## GO_NUCLEAR_EXPORT 69
## GO_RESPONSE_TO_INTERLEUKIN_1 36
## GO_REGULATION_OF_MRNA_CATABOLIC_PROCESS 61
## GO_CELLULAR_KETONE_METABOLIC_PROCESS 38
## GO_ESTABLISHMENT_OF_RNA_LOCALIZATION 69Visualize enrichment results.
Barplot
require(ggplot2)
df = hgtRes1@result
df$logFDR = -log10(df$p.adjust)
p = BarView(df[1:5,], "Description", 'logFDR')
p = p + labs(x = NULL) + coord_flip()
p
# Or use function barplot from enrichplot package
barplot(hgtRes1, showCategory = 5)
Dot plot
EnrichedView(hgtRes1, bottom = 5, mode = 1)
EnrichedView(hgtRes1, bottom = 5, mode = 2)
dotplot(hgtRes1, showCategory = 5)
Visualization functions from [enrichplot] (https://yulab-smu.github.io/clusterProfiler-book/chapter12.html).
hgtRes1@result$geneID = hgtRes1@result$geneName
#cnetplot
cnetplot(hgtRes1, 2)
heatplot(hgtRes1, showCategory = 3, foldChange=genelist)
emapplot(hgtRes1, layout="kk")
Visulization for GSEA enriched categories
#gseaplot
gseaplot(gseRes1, geneSetID = 1, title = gseRes1$Description[1])
gseaplot(gseRes1, geneSetID = 1, by = "runningScore", title = gseRes1$Description[1])
gseaplot(gseRes1, geneSetID = 1, by = "preranked", title = gseRes1$Description[1])
#or
gseaplot2(gseRes1, geneSetID = 1:3)
Type of gene sets for enrichment analysis
For enrichment analysis, MAGeCKFlute signifies the public available gene sets, including Pathways (PID, KEGG, REACTOME, BIOCARTA, C2CP), GO terms (GOBP, GOCC, GOMF), Complexes (CORUM, CPX) and molecular signature from MsigDB (c1, c2, c3, c4, c6, c7, HALLMARK).
Functional enrichment analysis on GO terms and pathways
Analysis of high-throughput data increasingly relies on pathway annotation and functional information derived from Gene Ontology, which is also useful in the analysis of CRISPR screens.
## KEGG and REACTOME pathways
enrich = EnrichAnalyzer(geneList = genelist[genelist< -1], type = "KEGG+REACTOME")
EnrichedView(enrich, bottom = 5)
## Only KEGG pathways
enrich = EnrichAnalyzer(geneList = genelist[genelist< -1], type = "KEGG")
EnrichedView(enrich, bottom = 5)
## Gene ontology
enrichGo = EnrichAnalyzer(genelist[genelist< -1], type = "GOBP+GOMF")
EnrichedView(enrichGo, bottom = 5)
Protein complex analysis
Functional annotations from the pathways and GO are powerful in the context of network dynamics. However, the approach has limitations in particular for the analysis of CRISPR screenings, in which elements within a protein complex rather than complete pathways might have a strong selection. So we incorporate protein complex resource from CORUM and CPX database, which enable identification of essential protein complexes from the CRISPR screens.
enrichPro = EnrichAnalyzer(genelist[genelist< -1], type = "CORUM+CPX")
EnrichedView(enrichPro, bottom = 5)
Enrichment analysis on the combination of the gene sets
enrichComb = EnrichAnalyzer(genelist[genelist< -1], type = "GOBP+KEGG")
EnrichedView(enrichComb, bottom = 5)
Limit the size of gene sets for testing
enrich = EnrichAnalyzer(genelist[genelist< -1], type = "GOBP", limit = c(1, 80))
EnrichedView(enrich, bottom = 5)
Remove redundant results using EnrichedFilter.
enrich1 = EnrichAnalyzer(genelist[genelist< -1], type = "GOMF+GOBP")
enrich2 = EnrichAnalyzer(genelist[genelist< -1], type = "GOMF+GOBP", filter = TRUE)
enrich3 = EnrichedFilter(enrich1)
EnrichedView(enrich1, bottom = 15)
EnrichedView(enrich2, bottom = 15)
EnrichedView(enrich3, bottom = 15)
Session info
sessionInfo()## R version 3.5.0 (2018-04-23)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggplot2_3.1.0 MAGeCKFlute_1.6.5
##
## loaded via a namespace (and not attached):
## [1] fgsea_1.8.0 colorspace_1.4-1 class_7.3-14
## [4] modeltools_0.2-22 ggridges_0.5.1 mclust_5.4.2
## [7] rprojroot_1.3-2 qvalue_2.14.0 XVector_0.22.0
## [10] ggpubr_0.2 farver_1.1.0 urltools_1.7.1
## [13] ggrepel_0.8.0 flexmix_2.3-14 bit64_0.9-7
## [16] mvtnorm_1.0-8 AnnotationDbi_1.44.0 xml2_1.2.0
## [19] codetools_0.2-15 splines_3.5.0 robustbase_0.93-3
## [22] GOSemSim_2.8.0 knitr_1.20 pathview_1.22.0
## [25] jsonlite_1.5 annotate_1.60.0 kernlab_0.9-27
## [28] cluster_2.0.7-1 GO.db_3.7.0 png_0.1-7
## [31] pheatmap_1.0.10 graph_1.60.0 ggforce_0.1.3
## [34] msigdbr_7.0.1 compiler_3.5.0 httr_1.3.1
## [37] rvcheck_0.1.1 backports_1.1.2 assertthat_0.2.0
## [40] Matrix_1.2-15 lazyeval_0.2.1 limma_3.38.2
## [43] tweenr_1.0.0 htmltools_0.3.6 prettyunits_1.0.2
## [46] tools_3.5.0 igraph_1.2.2 gtable_0.2.0
## [49] glue_1.3.0 reshape2_1.4.3 DO.db_2.9
## [52] dplyr_0.8.3 fastmatch_1.1-0 Rcpp_1.0.2
## [55] enrichplot_1.2.0 Biobase_2.42.0 trimcluster_0.1-2.1
## [58] Biostrings_2.50.2 nlme_3.1-137 fpc_2.1-11.1
## [61] ggraph_1.0.2 stringr_1.4.0 clusterProfiler_3.13.0
## [64] XML_3.98-1.16 dendextend_1.9.0 DOSE_3.11.2
## [67] DEoptimR_1.0-8 europepmc_0.3 zlibbioc_1.28.0
## [70] MASS_7.3-51.1 scales_1.0.0 hms_0.4.2
## [73] parallel_3.5.0 KEGGgraph_1.42.0 RColorBrewer_1.1-2
## [76] yaml_2.2.0 memoise_1.1.0 gridExtra_2.3
## [79] UpSetR_1.3.3 biomaRt_2.38.0 triebeard_0.3.0
## [82] stringi_1.2.4 RSQLite_2.1.1 genefilter_1.64.0
## [85] S4Vectors_0.20.1 BiocGenerics_0.28.0 BiocParallel_1.16.2
## [88] matrixStats_0.54.0 rlang_0.4.5 pkgconfig_2.0.2
## [91] prabclus_2.2-6 bitops_1.0-6 evaluate_0.12
## [94] lattice_0.20-38 purrr_0.2.5 labeling_0.3
## [97] cowplot_0.9.3 bit_1.1-14 tidyselect_0.2.5
## [100] ggsci_2.9 plyr_1.8.4 magrittr_1.5
## [103] R6_2.3.0 IRanges_2.16.0 DBI_1.0.0
## [106] withr_2.1.2 mgcv_1.8-26 pillar_1.4.2
## [109] whisker_0.3-2 units_0.6-1 survival_2.43-3
## [112] KEGGREST_1.22.0 RCurl_1.95-4.11 nnet_7.3-12
## [115] tibble_2.1.3 crayon_1.3.4 rmarkdown_1.10
## [118] viridis_0.5.1 progress_1.2.0 grid_3.5.0
## [121] sva_3.30.0 data.table_1.11.8 blob_1.1.1
## [124] Rgraphviz_2.26.0 diptest_0.75-7 digest_0.6.18
## [127] xtable_1.8-3 tidyr_0.8.2 gridGraphics_0.3-0
## [130] stats4_3.5.0 munsell_0.5.0 viridisLite_0.3.0
## [133] ggplotify_0.0.3